Diff of the two buildlogs: -- --- b1/build.log 2021-08-25 03:36:19.086396070 +0000 +++ b2/build.log 2021-08-25 03:40:16.657494153 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Aug 24 15:22:59 -12 2021 -I: pbuilder-time-stamp: 1629861779 +I: Current time: Tue Sep 27 23:59:22 +14 2022 +I: pbuilder-time-stamp: 1664272762 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -16,8 +16,8 @@ I: copying [./prime-phylo_1.0.11-9.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.1WZ8H2n9/trustedkeys.kbx': General error -gpgv: Signature made Sun Jul 26 22:24:25 2020 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.HnKe17DA/trustedkeys.kbx': General error +gpgv: Signature made Tue Jul 28 00:24:25 2020 +14 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "npatra974@gmail.com" gpgv: Can't check signature: No public key @@ -32,135 +32,169 @@ dpkg-source: info: applying 0004-fix-gcc10-build.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1267/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3522/tmp/hooks/D01_modify_environment starting +debug: Running on codethink15-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/3522/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3522/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=8' - DISTRIBUTION='' - HOME='/var/lib/jenkins' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/var/lib/jenkins + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='1267' - PS1='# ' - PS2='> ' + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=3522 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.B65vDXE14E/pbuilderrc_5JD0 --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.B65vDXE14E/b1 --logfile b1/build.log prime-phylo_1.0.11-9.dsc' - SUDO_GID='117' - SUDO_UID='110' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - USERNAME='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.16:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.B65vDXE14E/pbuilderrc_0cBM --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.B65vDXE14E/b2 --logfile b2/build.log prime-phylo_1.0.11-9.dsc' + SUDO_GID=117 + SUDO_UID=110 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + USERNAME=root + _='I: set' + http_proxy=http://192.168.101.16:3128 I: uname -a - Linux codethink12-arm64 4.15.0-154-generic #161-Ubuntu SMP Fri Jul 30 13:01:15 UTC 2021 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-154-generic #161-Ubuntu SMP Fri Jul 30 13:01:15 UTC 2021 aarch64 GNU/Linux I: ls -l /bin total 5252 - -rwxr-xr-x 1 root root 1282512 Aug 4 08:25 bash - -rwxr-xr-x 3 root root 34808 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 34808 Jul 20 2020 bzcat - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep - -rwxr-xr-x 3 root root 34808 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 14264 Jul 20 2020 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore - -rwxr-xr-x 1 root root 39832 Sep 22 2020 cat - -rwxr-xr-x 1 root root 64512 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 60368 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 64528 Sep 22 2020 chown - -rwxr-xr-x 1 root root 138896 Sep 22 2020 cp - -rwxr-xr-x 1 root root 129544 Dec 10 2020 dash - -rwxr-xr-x 1 root root 101384 Sep 22 2020 date - -rwxr-xr-x 1 root root 80984 Sep 22 2020 dd - -rwxr-xr-x 1 root root 89824 Sep 22 2020 df - -rwxr-xr-x 1 root root 143088 Sep 22 2020 dir - -rwxr-xr-x 1 root root 76152 Jul 28 07:09 dmesg - lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname - -rwxr-xr-x 1 root root 35632 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 31512 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 64856 Jul 28 07:09 findmnt - -rwsr-xr-x 1 root root 34824 Feb 26 04:12 fusermount - -rwxr-xr-x 1 root root 178400 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe - -rwxr-xr-x 1 root root 93744 Mar 2 11:30 gzip - -rwxr-xr-x 1 root root 18440 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 68720 Sep 22 2020 ln - -rwxr-xr-x 1 root root 52720 Feb 7 2020 login - -rwxr-xr-x 1 root root 143088 Sep 22 2020 ls - -rwxr-xr-x 1 root root 161960 Jul 28 07:09 lsblk - -rwxr-xr-x 1 root root 85200 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 68744 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 43976 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 51368 Jul 28 07:09 more - -rwsr-xr-x 1 root root 51360 Jul 28 07:09 mount - -rwxr-xr-x 1 root root 14496 Jul 28 07:09 mountpoint - -rwxr-xr-x 1 root root 134808 Sep 22 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 35720 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Aug 4 08:25 rbash -> bash - -rwxr-xr-x 1 root root 43872 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 68592 Sep 22 2020 rm - -rwxr-xr-x 1 root root 43880 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 19208 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Aug 20 21:24 sh -> dash - -rwxr-xr-x 1 root root 35656 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 72640 Sep 22 2020 stty - -rwsr-xr-x 1 root root 67776 Jul 28 07:09 su - -rwxr-xr-x 1 root root 35672 Sep 22 2020 sync - -rwxr-xr-x 1 root root 535768 Feb 16 2021 tar - -rwxr-xr-x 1 root root 10568 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 89120 Sep 22 2020 touch - -rwxr-xr-x 1 root root 31512 Sep 22 2020 true - -rwxr-xr-x 1 root root 14264 Feb 26 04:12 ulockmgr_server - -rwsr-xr-x 1 root root 30880 Jul 28 07:09 umount - -rwxr-xr-x 1 root root 35640 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress - -rwxr-xr-x 1 root root 143088 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 59584 Jul 28 07:09 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless - -rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew -I: user script /srv/workspace/pbuilder/1267/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1282512 Aug 5 2021 bash + -rwxr-xr-x 3 root root 34808 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 34808 Jul 21 2020 bzcat + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep + -rwxr-xr-x 3 root root 34808 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 14264 Jul 21 2020 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore + -rwxr-xr-x 1 root root 39832 Sep 23 2020 cat + -rwxr-xr-x 1 root root 64512 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 60368 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 64528 Sep 23 2020 chown + -rwxr-xr-x 1 root root 138896 Sep 23 2020 cp + -rwxr-xr-x 1 root root 129544 Dec 11 2020 dash + -rwxr-xr-x 1 root root 101384 Sep 23 2020 date + -rwxr-xr-x 1 root root 80984 Sep 23 2020 dd + -rwxr-xr-x 1 root root 89824 Sep 23 2020 df + -rwxr-xr-x 1 root root 143088 Sep 23 2020 dir + -rwxr-xr-x 1 root root 76152 Jul 29 2021 dmesg + lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname + -rwxr-xr-x 1 root root 35632 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 31512 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 64856 Jul 29 2021 findmnt + -rwsr-xr-x 1 root root 34824 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 178400 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 2021 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 2021 gzexe + -rwxr-xr-x 1 root root 93744 Mar 3 2021 gzip + -rwxr-xr-x 1 root root 18440 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 68720 Sep 23 2020 ln + -rwxr-xr-x 1 root root 52720 Feb 8 2020 login + -rwxr-xr-x 1 root root 143088 Sep 23 2020 ls + -rwxr-xr-x 1 root root 161960 Jul 29 2021 lsblk + -rwxr-xr-x 1 root root 85200 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 68744 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 43976 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 51368 Jul 29 2021 more + -rwsr-xr-x 1 root root 51360 Jul 29 2021 mount + -rwxr-xr-x 1 root root 14496 Jul 29 2021 mountpoint + -rwxr-xr-x 1 root root 134808 Sep 23 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 2021 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 35720 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Aug 5 2021 rbash -> bash + -rwxr-xr-x 1 root root 43872 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 68592 Sep 23 2020 rm + -rwxr-xr-x 1 root root 43880 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 19208 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 114016 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Sep 27 23:59 sh -> bash + lrwxrwxrwx 1 root root 4 Sep 24 05:47 sh.distrib -> dash + -rwxr-xr-x 1 root root 35656 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 72640 Sep 23 2020 stty + -rwsr-xr-x 1 root root 67776 Jul 29 2021 su + -rwxr-xr-x 1 root root 35672 Sep 23 2020 sync + -rwxr-xr-x 1 root root 535768 Feb 17 2021 tar + -rwxr-xr-x 1 root root 10568 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 89120 Sep 23 2020 touch + -rwxr-xr-x 1 root root 31512 Sep 23 2020 true + -rwxr-xr-x 1 root root 14264 Feb 27 2021 ulockmgr_server + -rwsr-xr-x 1 root root 30880 Jul 29 2021 umount + -rwxr-xr-x 1 root root 35640 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress + -rwxr-xr-x 1 root root 143088 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 59584 Jul 29 2021 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 2021 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 2021 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 2021 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 2021 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 2021 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 2021 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 2021 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 2021 zless + -rwxr-xr-x 1 root root 1842 Mar 3 2021 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 2021 znew +I: user script /srv/workspace/pbuilder/3522/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -342,7 +376,7 @@ Get: 118 http://deb.debian.org/debian bullseye/main arm64 liblapack3 arm64 3.9.0-3 [1541 kB] Get: 119 http://deb.debian.org/debian bullseye/main arm64 liblapack-dev arm64 3.9.0-3 [2758 kB] Get: 120 http://deb.debian.org/debian bullseye/main arm64 libxml2-dev arm64 2.9.10+dfsg-6.7 [754 kB] -Fetched 75.2 MB in 2s (47.8 MB/s) +Fetched 75.2 MB in 1s (55.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19646 files and directories currently installed.) @@ -848,7 +882,8 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/prime-phylo-1.0.11/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../prime-phylo_1.0.11-9_source.changes +hostname: Temporary failure in name resolution +I: Running cd /build/prime-phylo-1.0.11/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../prime-phylo_1.0.11-9_source.changes dpkg-buildpackage: info: source package prime-phylo dpkg-buildpackage: info: source version 1.0.11-9 dpkg-buildpackage: info: source distribution unstable @@ -1019,34 +1054,34 @@ make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' make -f src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/build.make src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/build make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' -[ 2%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/sfile.c.o [ 2%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gbread.c.o -cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile -I/build/prime-phylo-1.0.11/src/cxx/libraries/sfile -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo-sfile.dir/gbread.c.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/sfile/gbread.c -cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile -I/build/prime-phylo-1.0.11/src/cxx/libraries/sfile -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo-sfile.dir/sfile.c.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c +[ 2%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/sfile.c.o [ 2%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o -cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile -I/build/prime-phylo-1.0.11/src/cxx/libraries/sfile -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o -c /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile/gb.tab.c [ 3%] Building C object src/cxx/libraries/sfile/CMakeFiles/prime-phylo-sfile.dir/lexer.c.o +cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile -I/build/prime-phylo-1.0.11/src/cxx/libraries/sfile -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo-sfile.dir/sfile.c.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c +cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile -I/build/prime-phylo-1.0.11/src/cxx/libraries/sfile -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo-sfile.dir/gbread.c.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/sfile/gbread.c cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile -I/build/prime-phylo-1.0.11/src/cxx/libraries/sfile -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo-sfile.dir/lexer.c.o -c /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile/lexer.c +cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile && /usr/bin/cc -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_sfile_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile -I/build/prime-phylo-1.0.11/src/cxx/libraries/sfile -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -I/usr/lib/aarch64-linux-gnu/openmpi/include -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -o CMakeFiles/prime-phylo-sfile.dir/gb.tab.c.o -c /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile/gb.tab.c /build/prime-phylo-1.0.11/src/cxx/libraries/sfile/gbread.c: In function 'main': /build/prime-phylo-1.0.11/src/cxx/libraries/sfile/gbread.c:17:10: warning: implicit declaration of function 'strcmp' [-Wimplicit-function-declaration] 17 | if (!strcmp(argv[opt], "-d")) { | ^~~~~~ +/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile/gb.tab.c: In function 'yyparse': +/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile/gb.tab.c:1105:16: warning: implicit declaration of function 'yylex' [-Wimplicit-function-declaration] + 1105 | yychar = yylex (); + | ^~~~~ +gb.y: In function 'yyerror': +gb.y:291:70: warning: implicit declaration of function 'linenumber' [-Wimplicit-function-declaration] /build/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c: In function 'seq_print': /build/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c:265:14: warning: format '%d' expects argument of type 'int', but argument 2 has type 'long int' [-Wformat=] 265 | printf("%9d", char_counter + 1); | ^~~~~ ~~~~~~~~~~~~~~~~ | | | long int +gb.y: In function 'add_to_seq': /build/prime-phylo-1.0.11/src/cxx/libraries/sfile/sfile.c:212:15: warning: variable 'date' set but not used [-Wunused-but-set-variable] 212 | char *top, *date; | ^~~~ -/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile/gb.tab.c: In function 'yyparse': -/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile/gb.tab.c:1105:16: warning: implicit declaration of function 'yylex' [-Wimplicit-function-declaration] - 1105 | yychar = yylex (); - | ^~~~~ -gb.y: In function 'yyerror': -gb.y:291:70: warning: implicit declaration of function 'linenumber' [-Wimplicit-function-declaration] -gb.y: In function 'add_to_seq': gb.y:402:9: warning: unused variable 'new_buf' [-Wunused-variable] seqreader.l: In function 'seq_read': seqreader.l:270:9: warning: unused variable 'code' [-Wunused-variable] @@ -1064,10 +1099,10 @@ [ 4%] Built target prime-phylo-sfile make -f src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build.make src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/depend make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' -[ 5%] [FLEX][MyScanner] Building scanner with flex 2.6.4 -cd /build/prime-phylo-1.0.11/src/cxx/libraries/prime && /usr/bin/flex -Pyytree_ -o/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime/lexer.c NHX.l [ 5%] [BISON][MyParser] Building parser with bison 3.7.5 +[ 5%] [FLEX][MyScanner] Building scanner with flex 2.6.4 cd /build/prime-phylo-1.0.11/src/cxx/libraries/prime && /usr/bin/bison -d -y -p yytree_ -d -o /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime/NHXparse.c NHXparse.y +cd /build/prime-phylo-1.0.11/src/cxx/libraries/prime && /usr/bin/flex -Pyytree_ -o/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime/lexer.c NHX.l NHXparse.y:105.1-7: warning: POSIX Yacc does not support %expect [-Wyacc] 105 | %expect 4 | ^~~~~~~ @@ -1078,21 +1113,21 @@ make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' make -f src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build.make src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/build make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' -[ 6%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXnode.c.o -[ 6%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/lexer.c.o -cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/NHXnode.c.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXnode.c -[ 7%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXparse.c.o -cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/lexer.c.o -c /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime/lexer.c -cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/NHXparse.c.o -c /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime/NHXparse.c +[ 7%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXtree.c.o +[ 7%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXannotation.c.o +[ 7%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXnode.c.o [ 7%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/AnError.cc.o -[ 8%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Beep.cc.o +cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/NHXnode.c.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXnode.c +cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/NHXtree.c.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXtree.c +cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/NHXannotation.c.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXannotation.c cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/AnError.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/AnError.cc -[ 9%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXannotation.c.o -[ 9%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXtree.c.o +[ 8%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NHXparse.c.o +cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/NHXparse.c.o -c /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime/NHXparse.c +[ 8%] Building C object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/lexer.c.o +cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/lexer.c.o -c /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime/lexer.c +[ 9%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Beep.cc.o [ 10%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BeepOption.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/Beep.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Beep.cc -cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/NHXannotation.c.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXannotation.c -cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/NHXtree.c.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXtree.c cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/BeepOption.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepOption.cc /build/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXnode.c: In function 'NHX_debug_print': /build/prime-phylo-1.0.11/src/cxx/libraries/prime/NHXnode.c:155:25: warning: format '%d' expects argument of type 'int', but argument 3 has type 'double' [-Wformat=] @@ -1245,6 +1280,8 @@ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ODESolver.hh:396:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::ODESolver::D7' of non-integral type [-fpermissive] 396 | static const Real D7 = 69997945.0 / 29380423.0; | ^~ +[ 13%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscreteGamma.cc.o +cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/DiscreteGamma.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/DiscreteGamma.cc In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/PrimeOptionMap.cc:3: /build/prime-phylo-1.0.11/src/cxx/libraries/prime/PrimeOption.hh: In member function 'void beep::UserSubstitutionMatrixOption::parseParams(std::string&, unsigned int, std::vector&)': /build/prime-phylo-1.0.11/src/cxx/libraries/prime/PrimeOption.hh:405:23: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=] @@ -1253,10 +1290,8 @@ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/PrimeOption.hh:423:23: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=] 423 | catch(std::exception e) | ^ -[ 13%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Probability.cc.o +[ 14%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Probability.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/Probability.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Probability.cc -[ 14%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscreteGamma.cc.o -cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/DiscreteGamma.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/DiscreteGamma.cc [ 14%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Tokenizer.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/Tokenizer.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Tokenizer.cc [ 15%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TimeEstimator.cc.o @@ -1292,12 +1327,12 @@ cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/RandomTreeGenerator.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/RandomTreeGenerator.cc [ 22%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/StrStrMap.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/StrStrMap.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/StrStrMap.cc +[ 23%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Tree.cc.o +cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/Tree.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.cc In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.cc:7: /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.hh:54:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::EpochTree::MIN_SPLICE_DELTA' of non-integral type [-fpermissive] 54 | static const Real MIN_SPLICE_DELTA = 0.0001; | ^~~~~~~~~~~~~~~~ -[ 23%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Tree.cc.o -cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/Tree.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Tree.cc [ 23%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeAnalysis.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/TreeAnalysis.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeAnalysis.cc [ 24%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeDiscretizer.cc.o @@ -1312,6 +1347,8 @@ cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/TreeInputOutput.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeInputOutput.cc [ 27%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreeIOTraits.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/TreeIOTraits.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeIOTraits.cc +[ 28%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreePerturbationEvent.cc.o +cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/TreePerturbationEvent.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreePerturbationEvent.cc /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.cc: In constructor 'beep::TreeMCMC::TreeMCMC(beep::MCMCModel&, beep::Tree&, const Real&)': /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeMCMC.cc:26:15: warning: passing NULL to non-pointer argument 1 of 'beep::RealVector::RealVector(unsigned int)' [-Wconversion-null] 26 | old_times(NULL), @@ -1340,16 +1377,14 @@ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BeepVector.hh:257:25: note: declared here 257 | RealVector(unsigned n_elems) //!< All elems are initialized to zero. | ~~~~~~~~~^~~~~~~ -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeInputOutput.cc: In member function 'void beep::TreeInputOutput::fromFileStream(FILE*, beep::inputFormats)': -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeInputOutput.cc:118:22: warning: converting to non-pointer type 'char' from NULL [-Wconversion-null] - 118 | buf[ bytes_read ]=NULL; - | ^~~~ -[ 28%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/TreePerturbationEvent.cc.o -cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/TreePerturbationEvent.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreePerturbationEvent.cc [ 28%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ConstRateModel.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/ConstRateModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ConstRateModel.cc [ 29%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2P_common.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/Density2P_common.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_common.cc +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeInputOutput.cc: In member function 'void beep::TreeInputOutput::fromFileStream(FILE*, beep::inputFormats)': +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeInputOutput.cc:118:22: warning: converting to non-pointer type 'char' from NULL [-Wconversion-null] + 118 | buf[ bytes_read ]=NULL; + | ^~~~ [ 29%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2P_positive.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/Density2P_positive.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/Density2P_positive.cc [ 30%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/Density2PMCMC.cc.o @@ -1368,14 +1403,14 @@ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/LogNormDensity.hh:81:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::LogNormDensity::pi' of non-integral type [-fpermissive] 81 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. | ^~ -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeInputOutput.cc: In member function 'beep::Node* beep::TreeInputOutput::extendBeepTree(beep::Tree&, xmlNodePtr, const beep::TreeIOTraits&, std::vector*, beep::StrStrMap*, std::map*, std::map*)': -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeInputOutput.cc:1049:22: warning: 'idInt' may be used uninitialized in this function [-Wmaybe-uninitialized] - 1049 | new_node = S.addNode(l, r, idInt, name); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ [ 32%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeWeightHandler.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/EdgeWeightHandler.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightHandler.cc [ 33%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EdgeWeightMCMC.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/EdgeWeightMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightMCMC.cc +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeInputOutput.cc: In member function 'beep::Node* beep::TreeInputOutput::extendBeepTree(beep::Tree&, xmlNodePtr, const beep::TreeIOTraits&, std::vector*, beep::StrStrMap*, std::map*, std::map*)': +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/TreeInputOutput.cc:1049:22: warning: 'idInt' may be used uninitialized in this function [-Wmaybe-uninitialized] + 1049 | new_node = S.addNode(l, r, idInt, name); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeRateMCMC_common.cc: In member function 'void beep::EdgeRateMCMC_common::generateRates() [with Templ_EdgeRateModel = beep::gbmRateModel]': /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeRateMCMC_common.cc:104:30: warning: unused variable 'fparam' [-Wunused-variable] 104 | Real fparam = std::log(rate) - 0.5 * variance * (rtime - 3.0 * ltime); @@ -1389,24 +1424,24 @@ cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/InvGaussDensity.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/InvGaussDensity.cc [ 34%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LengthRateModel.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/LengthRateModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/LengthRateModel.cc +[ 35%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LogNormDensity.cc.o +cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/LogNormDensity.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/LogNormDensity.cc /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightMCMC.cc: In member function 'void beep::EdgeWeightMCMC::showCurrentTree()': /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeWeightMCMC.cc:106:27: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 106 | for (int i = 0; i < t.size(); i++) | ~~^~~~~~~~~~ -[ 35%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LogNormDensity.cc.o -cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/LogNormDensity.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/LogNormDensity.cc In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/InvGaussDensity.cc:1: /build/prime-phylo-1.0.11/src/cxx/libraries/prime/InvGaussDensity.hh:89:25: warning: 'constexpr' needed for in-class initialization of static data member 'const double beep::InvGaussDensity::pi' of non-integral type [-fpermissive] 89 | static const double pi = 3.14159265358979; //!< math.constant \f$\pi\f$ | ^~ [ 36%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/NormalDensity.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/NormalDensity.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.cc -[ 36%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/UniformDensity.cc.o -cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/UniformDensity.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/UniformDensity.cc In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/LogNormDensity.cc:1: /build/prime-phylo-1.0.11/src/cxx/libraries/prime/LogNormDensity.hh:81:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::LogNormDensity::pi' of non-integral type [-fpermissive] 81 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. | ^~ +[ 36%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/UniformDensity.cc.o +cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/UniformDensity.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/UniformDensity.cc [ 37%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/VarRateModel.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/VarRateModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/VarRateModel.cc [ 37%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SiteRateHandler.cc.o @@ -1425,22 +1460,14 @@ cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/MCMCObject.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/MCMCObject.cc [ 40%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleMCMC.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/SimpleMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SimpleMCMC.cc -[ 41%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleMCMCPostSample.cc.o -cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/SimpleMCMCPostSample.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SimpleMCMCPostSample.cc -[ 41%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleML.cc.o -cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/SimpleML.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SimpleML.cc In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.cc:7: /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.hh:83:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::SiteRateHandler::MAX' of non-integral type [-fpermissive] 83 | static const Real MAX = 1e10; //!< rates do not change for alpha > MAX. | ^~~ -In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/StdMCMCModel.cc:5: -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/LogNormDensity.hh:81:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::LogNormDensity::pi' of non-integral type [-fpermissive] - 81 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. - | ^~ -In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/StdMCMCModel.cc:6: -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.hh:84:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::NormalDensity::pi' of non-integral type [-fpermissive] - 84 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. - | ^~ +[ 41%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleMCMCPostSample.cc.o +cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/SimpleMCMCPostSample.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SimpleMCMCPostSample.cc +[ 41%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SimpleML.cc.o +cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/SimpleML.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SimpleML.cc [ 42%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/mcmc/MCMCSampler.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/mcmc/MCMCSampler.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/mcmc/MCMCSampler.cc [ 43%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/mcmc/GSRSampler.cc.o @@ -1451,12 +1478,20 @@ cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/SimpleObserver.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SimpleObserver.cc [ 44%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MpiMCMC.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/MpiMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/MpiMCMC.cc +In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/StdMCMCModel.cc:5: +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/LogNormDensity.hh:81:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::LogNormDensity::pi' of non-integral type [-fpermissive] + 81 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. + | ^~ +In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/StdMCMCModel.cc:6: +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/NormalDensity.hh:84:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::NormalDensity::pi' of non-integral type [-fpermissive] + 84 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. + | ^~ +[ 45%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MultiGSR.cc.o +cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/MultiGSR.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/MultiGSR.cc /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SimpleMCMC.cc: In member function 'virtual void beep::SimpleMCMC::iterate(unsigned int, unsigned int)': /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SimpleMCMC.cc:78:14: warning: variable 'check_number_nonupdate' set but not used [-Wunused-but-set-variable] 78 | unsigned check_number_nonupdate = 0; | ^~~~~~~~~~~~~~~~~~~~~~ -[ 45%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MultiGSR.cc.o -cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/MultiGSR.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/MultiGSR.cc [ 45%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MpiMultiGSR.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/MpiMultiGSR.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/MpiMultiGSR.cc [ 46%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BDTreeGenerator.cc.o @@ -1464,9 +1499,9 @@ [ 47%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathMCMC.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/BirthDeathMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathMCMC.cc [ 47%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathProbs.cc.o -cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/BirthDeathProbs.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathProbs.cc [ 48%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/CongruentGuestTreeTimeMCMC.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/CongruentGuestTreeTimeMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/CongruentGuestTreeTimeMCMC.cc +cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/BirthDeathProbs.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathProbs.cc [ 48%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DiscBirthDeathProbs.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/DiscBirthDeathProbs.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/DiscBirthDeathProbs.cc /build/prime-phylo-1.0.11/src/cxx/libraries/prime/MpiMultiGSR.cc: In member function 'virtual beep::Probability beep::MpiMultiGSR::calcDataProbability(unsigned int)': @@ -1598,20 +1633,8 @@ | ^~ [ 52%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/EpochDLTRS.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/EpochDLTRS.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochDLTRS.cc -In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:9, - from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTMCMC.hh:7, - from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTMCMC.cc:1: -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.hh:54:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::EpochTree::MIN_SPLICE_DELTA' of non-integral type [-fpermissive] - 54 | static const Real MIN_SPLICE_DELTA = 0.0001; - | ^~~~~~~~~~~~~~~~ -In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTMCMC.hh:7, - from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTMCMC.cc:1: -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:50:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::EpochBDTProbs::REL_TOL' of non-integral type [-fpermissive] - 50 | static const Real REL_TOL = 1e-6; - | ^~~~~~~ -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:55:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::EpochBDTProbs::ABS_TOL' of non-integral type [-fpermissive] - 55 | static const Real ABS_TOL = 1e-6; - | ^~~~~~~ +[ 52%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GammaMap.cc.o +cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/GammaMap.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaMap.cc In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:8: /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.hh: In constructor 'beep::EdgeDiscGSR::EdgeDiscGSR(beep::Tree*, beep::EdgeDiscTree*, beep::StrStrMap*, beep::Density2P*, beep::EdgeDiscBDProbs*, beep::UnsignedVector*)': /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.hh:588:14: warning: 'beep::EdgeDiscGSR::m_calculatedAtAndBelow' will be initialized after [-Wreorder] @@ -1640,8 +1663,20 @@ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EdgeDiscGSR.cc:897:18: warning: unused variable 'timeStep' [-Wunused-variable] 897 | Real timeStep = u->isLeaf() ? 1.0 : m_DS->getTimestep(xPoint.first); | ^~~~~~~~ -[ 52%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GammaMap.cc.o -cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/GammaMap.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/GammaMap.cc +In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:9, + from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTMCMC.hh:7, + from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTMCMC.cc:1: +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochTree.hh:54:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::EpochTree::MIN_SPLICE_DELTA' of non-integral type [-fpermissive] + 54 | static const Real MIN_SPLICE_DELTA = 0.0001; + | ^~~~~~~~~~~~~~~~ +In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTMCMC.hh:7, + from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTMCMC.cc:1: +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:50:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::EpochBDTProbs::REL_TOL' of non-integral type [-fpermissive] + 50 | static const Real REL_TOL = 1e-6; + | ^~~~~~~ +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:55:20: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::EpochBDTProbs::ABS_TOL' of non-integral type [-fpermissive] + 55 | static const Real ABS_TOL = 1e-6; + | ^~~~~~~ [ 53%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/GuestTreeModel.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/GuestTreeModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/GuestTreeModel.cc In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochBDTProbs.hh:7, @@ -1902,6 +1937,10 @@ cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/MaxReconciledTreeModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/MaxReconciledTreeModel.cc [ 57%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/PerturbationObservable.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/PerturbationObservable.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/PerturbationObservable.cc +[ 58%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciledTreeModel.cc.o +cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/ReconciledTreeModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeModel.cc +[ 58%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciledTreeTimeModel.cc.o +cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/ReconciledTreeTimeModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeTimeModel.cc /build/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.cc: In member function 'unsigned int beep::fastGEM::calcMaxProb(unsigned int)': /build/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.cc:136:14: warning: variable 'topRateProb' set but not used [-Wunused-but-set-variable] 136 | Probability topRateProb = df->operator()(rate); @@ -1918,10 +1957,6 @@ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/fastGEM.cc:1356:10: warning: variable 'zeroTotalQuotient' set but not used [-Wunused-but-set-variable] 1356 | Real zeroTotalQuotient = 0.0; | ^~~~~~~~~~~~~~~~~ -[ 58%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciledTreeModel.cc.o -cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/ReconciledTreeModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeModel.cc -[ 58%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciledTreeTimeModel.cc.o -cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/ReconciledTreeTimeModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeTimeModel.cc [ 59%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciledTreeTimeMCMC.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/ReconciledTreeTimeMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciledTreeTimeMCMC.cc [ 59%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationModel.cc.o @@ -1936,12 +1971,12 @@ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/LogNormDensity.hh:81:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::LogNormDensity::pi' of non-integral type [-fpermissive] 81 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. | ^~ +[ 62%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTimeSampler.cc.o +cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/ReconciliationTimeSampler.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeSampler.cc /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationSampler.cc: In member function 'void beep::ReconciliationSampler::setAttributesAndProbabilities()': /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationSampler.cc:161:17: warning: variable 'p' set but not used [-Wunused-but-set-variable] 161 | Probability p = calculateDataProbability(); | ^ -[ 62%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTimeSampler.cc.o -cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/ReconciliationTimeSampler.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeSampler.cc [ 62%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/ReconciliationTreeGenerator.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/ReconciliationTreeGenerator.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTreeGenerator.cc [ 63%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/DLRSOrthoCalculator.cc.o @@ -1960,14 +1995,14 @@ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTimeSampler.cc:422:58: warning: typedef 'MapIter' locally defined but not used [-Wunused-local-typedefs] 422 | typedef std::map::const_iterator MapIter; | ^~~~~~~ -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTreeGenerator.cc: In constructor 'beep::ReconciliationTreeGenerator::ReconciliationTreeGenerator(beep::BirthDeathProbs&, const string&)': -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTreeGenerator.cc:31:3: warning: 'beep::ReconciliationTreeGenerator::R' is initialized with itself [-Winit-self] - 31 | ReconciliationTreeGenerator:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 65%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTree.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/HybridTree.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.cc [ 66%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTreeIO.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/HybridTreeIO.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeIO.cc +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTreeGenerator.cc: In constructor 'beep::ReconciliationTreeGenerator::ReconciliationTreeGenerator(beep::BirthDeathProbs&, const string&)': +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/ReconciliationTreeGenerator.cc:31:3: warning: 'beep::ReconciliationTreeGenerator::R' is initialized with itself [-Winit-self] + 31 | ReconciliationTreeGenerator:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 66%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridTreeInputOutput.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/HybridTreeInputOutput.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTreeInputOutput.cc [ 67%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BDHybridTreeGenerator.cc.o @@ -1976,12 +2011,12 @@ cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/BirthDeathInHybridProbs.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridProbs.cc [ 68%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/BirthDeathInHybridMCMC.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/BirthDeathInHybridMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/BirthDeathInHybridMCMC.cc -[ 69%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridBDTreeGenerator.cc.o -cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/HybridBDTreeGenerator.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridBDTreeGenerator.cc /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.cc: In member function 'beep::Tree& beep::HybridTree::getBinaryTree() const': /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridTree.cc:367:40: warning: ISO C++ forbids comparison between pointer and integer [-fpermissive] 367 | if(rootNode && bTree.getRootNode() == false) | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~ +[ 69%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridBDTreeGenerator.cc.o +cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/HybridBDTreeGenerator.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridBDTreeGenerator.cc [ 69%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridGuestTreeMCMC.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/HybridGuestTreeMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/HybridGuestTreeMCMC.cc [ 70%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/HybridGuestTreeModel.cc.o @@ -2012,20 +2047,20 @@ /usr/include/c++/10/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp] 32 | #warning \ | ^~~~~~~ -[ 75%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MatrixTransitionHandler.cc.o -cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/MatrixTransitionHandler.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixTransitionHandler.cc In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/CacheSubstitutionModel.cc:9: /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.hh:83:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::SiteRateHandler::MAX' of non-integral type [-fpermissive] 83 | static const Real MAX = 1e10; //!< rates do not change for alpha > MAX. | ^~~ +[ 75%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/MatrixTransitionHandler.cc.o +cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/MatrixTransitionHandler.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/MatrixTransitionHandler.cc [ 75%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SeqIO.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/SeqIO.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SeqIO.cc -[ 76%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SequenceGenerator.cc.o -cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/SequenceGenerator.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceGenerator.cc In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/FastCacheSubstitutionModel.cc:9: /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.hh:83:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::SiteRateHandler::MAX' of non-integral type [-fpermissive] 83 | static const Real MAX = 1e10; //!< rates do not change for alpha > MAX. | ^~~ +[ 76%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SequenceGenerator.cc.o +cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/SequenceGenerator.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceGenerator.cc [ 77%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SequenceType.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/SequenceType.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceType.cc [ 77%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SequenceData.cc.o @@ -2034,11 +2069,6 @@ cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/SubstitutionModel.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SubstitutionModel.cc [ 78%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/SubstitutionMCMC.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/SubstitutionMCMC.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SubstitutionMCMC.cc -In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceGenerator.hh:15, - from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceGenerator.cc:4: -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.hh:83:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::SiteRateHandler::MAX' of non-integral type [-fpermissive] - 83 | static const Real MAX = 1e10; //!< rates do not change for alpha > MAX. - | ^~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceType.cc:270:10: warning: 'std::ostream& beep::operator<<(std::ostream&, const beep::SequenceType&)' has not been declared within 'beep' 270 | ostream& beep::operator<<(ostream& os, const SequenceType& dt) | ^~~~ @@ -2046,12 +2076,17 @@ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceType.hh:56:26: note: only here as a 'friend' 56 | friend std::ostream& operator<<(std::ostream& os, const SequenceType& dt); | ^~~~~~~~ -In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SubstitutionModel.cc:9: +In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceGenerator.hh:15, + from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceGenerator.cc:4: /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.hh:83:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::SiteRateHandler::MAX' of non-integral type [-fpermissive] 83 | static const Real MAX = 1e10; //!< rates do not change for alpha > MAX. | ^~~ [ 79%] Building CXX object src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/LA_Vector.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries -I/usr/lib/aarch64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -pthread -o CMakeFiles/prime-phylo.dir/LA_Vector.cc.o -c /build/prime-phylo-1.0.11/src/cxx/libraries/prime/LA_Vector.cc +In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SubstitutionModel.cc:9: +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.hh:83:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::SiteRateHandler::MAX' of non-integral type [-fpermissive] + 83 | static const Real MAX = 1e10; //!< rates do not change for alpha > MAX. + | ^~~ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceData.cc: In member function 'std::map beep::SequenceData::getBaseFrequencies()': /build/prime-phylo-1.0.11/src/cxx/libraries/prime/SequenceData.cc:288:31: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] 288 | for (int i = 0; i < seqType.alphabetSize(); i++) @@ -2077,105 +2112,105 @@ make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' [ 81%] Built target prime-phylo make -f src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/build.make src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/depend -make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' make -f src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/build.make src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/depend -make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' -cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-1.0.11 /build/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeDTLSR /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/DependInfo.cmake --color= make -f src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/build.make src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/depend make -f src/cxx/tools/treesize/CMakeFiles/treesize.dir/build.make src/cxx/tools/treesize/CMakeFiles/treesize.dir/depend -make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' -cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-1.0.11 /build/prime-phylo-1.0.11/src/cxx/applications/primeDLRS /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeDLRS /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/DependInfo.cmake --color= make -f src/cxx/tools/showtree/CMakeFiles/showtree.dir/build.make src/cxx/tools/showtree/CMakeFiles/showtree.dir/depend make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' -make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' make -f src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/build.make src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/depend +make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' +cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-1.0.11 /build/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeDTLSR /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/DependInfo.cmake --color= make -f src/cxx/tools/reroot/CMakeFiles/reroot.dir/build.make src/cxx/tools/reroot/CMakeFiles/reroot.dir/depend make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' +cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-1.0.11 /build/prime-phylo-1.0.11/src/cxx/applications/primeDLRS /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeDLRS /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' make -f src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/build.make src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/depend -Dependee "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/DependInfo.cmake" is newer than depender "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/depend.internal". -Dependee "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeDTLSR/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/depend.internal". +make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' +make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' +make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' [ 82%] Generating cmdline.c, cmdline.h +Dependee "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/DependInfo.cmake" is newer than depender "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/depend.internal". +Dependee "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeDTLSR/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/depend.internal". Dependee "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/DependInfo.cmake" is newer than depender "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/depend.internal". Dependee "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeDLRS/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/depend.internal". -[ 83%] Generating cmdline.c, cmdline.h -cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/treesize && /usr/bin/gengetopt -i /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/treesize/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/treesize -Scanning dependencies of target primeDTLSR cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeGEM && /usr/bin/gengetopt -i /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeGEM/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeGEM -make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' -make -f src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/build.make src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/build +[ 83%] Generating cmdline.c, cmdline.h +[ 83%] Generating cmdline.c, cmdline.h [ 84%] Generating cmdline.c, cmdline.h -make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' [ 84%] Generating cmdline.c, cmdline.h cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reroot && /usr/bin/gengetopt -i /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reroot/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reroot +cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/tree2leafnames && /usr/bin/gengetopt -i /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/tree2leafnames/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/tree2leafnames [ 85%] Generating cmdline.c, cmdline.h cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/showtree && /usr/bin/gengetopt -i /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/showtree/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/showtree +cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/treesize && /usr/bin/gengetopt -i /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/treesize/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/treesize cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile && /usr/bin/gengetopt -i /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile +Scanning dependencies of target primeDTLSR +make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' Scanning dependencies of target primeDLRS -[ 85%] Generating cmdline.c, cmdline.h +make -f src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/build.make src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/build make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' make -f src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/build.make src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/build make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' -cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/tree2leafnames && /usr/bin/gengetopt -i /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/tree2leafnames/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/tree2leafnames -cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-1.0.11 /build/prime-phylo-1.0.11/src/cxx/tools/treesize /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/treesize /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/treesize/CMakeFiles/treesize.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' [ 85%] Building CXX object src/cxx/applications/primeDTLSR/CMakeFiles/primeDTLSR.dir/idolatrous.cc.o +cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-1.0.11 /build/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/tree2leafnames /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/DependInfo.cmake --color= cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeDTLSR && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeDTLSR -I/build/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -pthread -o CMakeFiles/primeDTLSR.dir/idolatrous.cc.o -c /build/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc -cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-1.0.11 /build/prime-phylo-1.0.11/src/cxx/tools/reroot /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reroot /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reroot/CMakeFiles/reroot.dir/DependInfo.cmake --color= -Dependee "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/treesize/CMakeFiles/treesize.dir/DependInfo.cmake" is newer than depender "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/treesize/CMakeFiles/treesize.dir/depend.internal". -Dependee "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/treesize/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/treesize/CMakeFiles/treesize.dir/depend.internal". +cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-1.0.11 /build/prime-phylo-1.0.11/src/cxx/tools/reconcile /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/DependInfo.cmake --color= cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-1.0.11 /build/prime-phylo-1.0.11/src/cxx/applications/primeGEM /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeGEM /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/DependInfo.cmake --color= +cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-1.0.11 /build/prime-phylo-1.0.11/src/cxx/tools/treesize /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/treesize /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/treesize/CMakeFiles/treesize.dir/DependInfo.cmake --color= +cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-1.0.11 /build/prime-phylo-1.0.11/src/cxx/tools/reroot /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reroot /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reroot/CMakeFiles/reroot.dir/DependInfo.cmake --color= cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-1.0.11 /build/prime-phylo-1.0.11/src/cxx/tools/showtree /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/showtree /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/showtree/CMakeFiles/showtree.dir/DependInfo.cmake --color= -cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-1.0.11 /build/prime-phylo-1.0.11/src/cxx/tools/reconcile /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/DependInfo.cmake --color= -cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-1.0.11 /build/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/tree2leafnames /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/DependInfo.cmake --color= [ 85%] Building CXX object src/cxx/applications/primeDLRS/CMakeFiles/primeDLRS.dir/primeDLRS.cc.o -Scanning dependencies of target treesize +Dependee "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/treesize/CMakeFiles/treesize.dir/DependInfo.cmake" is newer than depender "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/treesize/CMakeFiles/treesize.dir/depend.internal". +Dependee "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/DependInfo.cmake" is newer than depender "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/depend.internal". +Dependee "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/depend.internal". +Dependee "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/treesize/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/treesize/CMakeFiles/treesize.dir/depend.internal". cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeDLRS && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeDLRS -I/build/prime-phylo-1.0.11/src/cxx/applications/primeDLRS -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -pthread -o CMakeFiles/primeDLRS.dir/primeDLRS.cc.o -c /build/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc +Dependee "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/DependInfo.cmake" is newer than depender "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/depend.internal". +Dependee "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeGEM/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/depend.internal". +Dependee "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/DependInfo.cmake" is newer than depender "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/depend.internal". +Dependee "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/tree2leafnames/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/depend.internal". +Scanning dependencies of target reconcile +Scanning dependencies of target treesize +make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' make -f src/cxx/tools/treesize/CMakeFiles/treesize.dir/build.make src/cxx/tools/treesize/CMakeFiles/treesize.dir/build +make -f src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/build.make src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/build +make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' -Dependee "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/showtree/CMakeFiles/showtree.dir/DependInfo.cmake" is newer than depender "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/showtree/CMakeFiles/showtree.dir/depend.internal". -Dependee "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/showtree/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/showtree/CMakeFiles/showtree.dir/depend.internal". -Dependee "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/DependInfo.cmake" is newer than depender "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/depend.internal". -Dependee "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeGEM/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/depend.internal". Dependee "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reroot/CMakeFiles/reroot.dir/DependInfo.cmake" is newer than depender "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reroot/CMakeFiles/reroot.dir/depend.internal". Dependee "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reroot/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reroot/CMakeFiles/reroot.dir/depend.internal". -Scanning dependencies of target showtree +Scanning dependencies of target tree2leafnames make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' -make -f src/cxx/tools/showtree/CMakeFiles/showtree.dir/build.make src/cxx/tools/showtree/CMakeFiles/showtree.dir/build +make -f src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/build.make src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/build Scanning dependencies of target primeGEM -Dependee "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/DependInfo.cmake" is newer than depender "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/depend.internal". -Dependee "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/tree2leafnames/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/depend.internal". -Dependee "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/DependInfo.cmake" is newer than depender "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/depend.internal". -Dependee "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/depend.internal". -make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' make -f src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/build.make src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/build make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' -Scanning dependencies of target reconcile +[ 86%] Building CXX object src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/Rootalyzer.cc.o +[ 86%] Building CXX object src/cxx/tools/treesize/CMakeFiles/treesize.dir/treesize.cc.o +cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile -I/build/prime-phylo-1.0.11/src/cxx/tools/reconcile -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -pthread -o CMakeFiles/reconcile.dir/Rootalyzer.cc.o -c /build/prime-phylo-1.0.11/src/cxx/tools/reconcile/Rootalyzer.cc +cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/treesize && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/treesize -I/build/prime-phylo-1.0.11/src/cxx/tools/treesize -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -pthread -o CMakeFiles/treesize.dir/treesize.cc.o -c /build/prime-phylo-1.0.11/src/cxx/tools/treesize/treesize.cc +make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' +Dependee "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/showtree/CMakeFiles/showtree.dir/DependInfo.cmake" is newer than depender "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/showtree/CMakeFiles/showtree.dir/depend.internal". +Dependee "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/showtree/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/showtree/CMakeFiles/showtree.dir/depend.internal". Scanning dependencies of target reroot -Scanning dependencies of target tree2leafnames make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' make -f src/cxx/tools/reroot/CMakeFiles/reroot.dir/build.make src/cxx/tools/reroot/CMakeFiles/reroot.dir/build -[ 86%] Building CXX object src/cxx/tools/showtree/CMakeFiles/showtree.dir/showtree.cc.o -cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/showtree && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/showtree -I/build/prime-phylo-1.0.11/src/cxx/tools/showtree -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -pthread -o CMakeFiles/showtree.dir/showtree.cc.o -c /build/prime-phylo-1.0.11/src/cxx/tools/showtree/showtree.cc -make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' +Scanning dependencies of target showtree make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' +make -f src/cxx/tools/showtree/CMakeFiles/showtree.dir/build.make src/cxx/tools/showtree/CMakeFiles/showtree.dir/build make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' -make -f src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/build.make src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/build -[ 86%] Building CXX object src/cxx/tools/treesize/CMakeFiles/treesize.dir/treesize.cc.o -make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' -make -f src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/build.make src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/build make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' -cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/treesize && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/treesize -I/build/prime-phylo-1.0.11/src/cxx/tools/treesize -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -pthread -o CMakeFiles/treesize.dir/treesize.cc.o -c /build/prime-phylo-1.0.11/src/cxx/tools/treesize/treesize.cc -[ 86%] Building CXX object src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/troyo.cc.o -cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeGEM && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeGEM -I/build/prime-phylo-1.0.11/src/cxx/applications/primeGEM -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -pthread -o CMakeFiles/primeGEM.dir/troyo.cc.o -c /build/prime-phylo-1.0.11/src/cxx/applications/primeGEM/troyo.cc -[ 86%] Building CXX object src/cxx/tools/reroot/CMakeFiles/reroot.dir/reroot.cc.o [ 87%] Building CXX object src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/tree2leafnames.cc.o +[ 86%] Building CXX object src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/troyo.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/tree2leafnames && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/tree2leafnames -I/build/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -pthread -o CMakeFiles/tree2leafnames.dir/tree2leafnames.cc.o -c /build/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames/tree2leafnames.cc +cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeGEM && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeGEM -I/build/prime-phylo-1.0.11/src/cxx/applications/primeGEM -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -pthread -o CMakeFiles/primeGEM.dir/troyo.cc.o -c /build/prime-phylo-1.0.11/src/cxx/applications/primeGEM/troyo.cc +[ 88%] Building CXX object src/cxx/tools/showtree/CMakeFiles/showtree.dir/showtree.cc.o +cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/showtree && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/showtree -I/build/prime-phylo-1.0.11/src/cxx/tools/showtree -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -pthread -o CMakeFiles/showtree.dir/showtree.cc.o -c /build/prime-phylo-1.0.11/src/cxx/tools/showtree/showtree.cc +[ 88%] Building CXX object src/cxx/tools/reroot/CMakeFiles/reroot.dir/reroot.cc.o cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reroot && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reroot -I/build/prime-phylo-1.0.11/src/cxx/tools/reroot -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -pthread -o CMakeFiles/reroot.dir/reroot.cc.o -c /build/prime-phylo-1.0.11/src/cxx/tools/reroot/reroot.cc -[ 88%] Building CXX object src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/Rootalyzer.cc.o -cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile -I/build/prime-phylo-1.0.11/src/cxx/tools/reconcile -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -pthread -o CMakeFiles/reconcile.dir/Rootalyzer.cc.o -c /build/prime-phylo-1.0.11/src/cxx/tools/reconcile/Rootalyzer.cc /build/prime-phylo-1.0.11/src/cxx/tools/showtree/showtree.cc: In function 'void outputSingleTree(beep::Tree&, beep::TreeIOTraits&, gengetopt_args_info&)': /build/prime-phylo-1.0.11/src/cxx/tools/showtree/showtree.cc:30:20: warning: variable 'nw' set but not used [-Wunused-but-set-variable] 30 | bool et, nt, bl, nw; @@ -2207,38 +2242,38 @@ cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/treesize && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/treesize -I/build/prime-phylo-1.0.11/src/cxx/tools/treesize -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -pthread -o CMakeFiles/treesize.dir/cmdline.c.o -c /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/treesize/cmdline.c [ 90%] Building C object src/cxx/tools/tree2leafnames/CMakeFiles/tree2leafnames.dir/cmdline.c.o cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/tree2leafnames && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/tree2leafnames -I/build/prime-phylo-1.0.11/src/cxx/tools/tree2leafnames -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -pthread -o CMakeFiles/tree2leafnames.dir/cmdline.c.o -c /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/tree2leafnames/cmdline.c -[ 91%] Linking CXX executable treesize -cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/treesize && /usr/bin/cmake -E cmake_link_script CMakeFiles/treesize.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic -pthread CMakeFiles/treesize.dir/treesize.cc.o CMakeFiles/treesize.dir/cmdline.c.o -o treesize -Wl,-rpath,/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime:/usr/lib/aarch64-linux-gnu/openmpi/lib:/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/aarch64-linux-gnu/libboost_mpi.so.1.74.0 /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.74.0 ../../libraries/sfile/libprime-phylo-sfile.so -[ 92%] Linking CXX executable showtree +[ 91%] Linking CXX executable showtree cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/showtree && /usr/bin/cmake -E cmake_link_script CMakeFiles/showtree.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic -pthread CMakeFiles/showtree.dir/showtree.cc.o CMakeFiles/showtree.dir/cmdline.c.o -o showtree -Wl,-rpath,/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime:/usr/lib/aarch64-linux-gnu/openmpi/lib:/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/aarch64-linux-gnu/libboost_mpi.so.1.74.0 /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.74.0 ../../libraries/sfile/libprime-phylo-sfile.so -[ 92%] Linking CXX executable tree2leafnames +[ 91%] Linking CXX executable tree2leafnames cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/tree2leafnames && /usr/bin/cmake -E cmake_link_script CMakeFiles/tree2leafnames.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic -pthread CMakeFiles/tree2leafnames.dir/tree2leafnames.cc.o CMakeFiles/tree2leafnames.dir/cmdline.c.o -o tree2leafnames -Wl,-rpath,/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime:/usr/lib/aarch64-linux-gnu/openmpi/lib:/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/aarch64-linux-gnu/libboost_mpi.so.1.74.0 /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.74.0 ../../libraries/sfile/libprime-phylo-sfile.so +[ 92%] Linking CXX executable treesize +cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/treesize && /usr/bin/cmake -E cmake_link_script CMakeFiles/treesize.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic -pthread CMakeFiles/treesize.dir/treesize.cc.o CMakeFiles/treesize.dir/cmdline.c.o -o treesize -Wl,-rpath,/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime:/usr/lib/aarch64-linux-gnu/openmpi/lib:/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/aarch64-linux-gnu/libboost_mpi.so.1.74.0 /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.74.0 ../../libraries/sfile/libprime-phylo-sfile.so make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' -[ 92%] Built target treesize +[ 92%] Built target showtree make -f src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/build.make src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/depend make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' -make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' [ 92%] Generating cmdline.c, cmdline.h -[ 92%] Built target tree2leafnames cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/chainsaw && /usr/bin/gengetopt -i /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/chainsaw/cmdline.ggo --file-name=cmdline --output-dir=/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/chainsaw -[ 92%] Building CXX object src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/reconcile.cc.o -cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile -I/build/prime-phylo-1.0.11/src/cxx/tools/reconcile -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -pthread -o CMakeFiles/reconcile.dir/reconcile.cc.o -c /build/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' +[ 92%] Built target treesize cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/prime-phylo-1.0.11 /build/prime-phylo-1.0.11/src/cxx/tools/chainsaw /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/chainsaw /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/DependInfo.cmake --color= -[ 92%] Built target showtree +[ 93%] Building C object src/cxx/tools/reroot/CMakeFiles/reroot.dir/cmdline.c.o +cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reroot && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reroot -I/build/prime-phylo-1.0.11/src/cxx/tools/reroot -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -pthread -o CMakeFiles/reroot.dir/cmdline.c.o -c /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reroot/cmdline.c +make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' Dependee "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/DependInfo.cmake" is newer than depender "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/depend.internal". Dependee "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/chainsaw/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/depend.internal". Scanning dependencies of target chainsaw make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' make -f src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/build.make src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/build -[ 93%] Building C object src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/cmdline.c.o make[3]: Entering directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' -cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile -I/build/prime-phylo-1.0.11/src/cxx/tools/reconcile -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -pthread -o CMakeFiles/reconcile.dir/cmdline.c.o -c /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile/cmdline.c [ 94%] Building CXX object src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/chainsaw.cc.o +[ 94%] Built target tree2leafnames cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/chainsaw && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/chainsaw -I/build/prime-phylo-1.0.11/src/cxx/tools/chainsaw -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -pthread -o CMakeFiles/chainsaw.dir/chainsaw.cc.o -c /build/prime-phylo-1.0.11/src/cxx/tools/chainsaw/chainsaw.cc +[ 94%] Building C object src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/cmdline.c.o +cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/chainsaw && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/chainsaw -I/build/prime-phylo-1.0.11/src/cxx/tools/chainsaw -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -pthread -o CMakeFiles/chainsaw.dir/cmdline.c.o -c /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/chainsaw/cmdline.c In file included from /build/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc:13: /build/prime-phylo-1.0.11/src/cxx/libraries/prime/InvGaussDensity.hh:89:25: warning: 'constexpr' needed for in-class initialization of static data member 'const double beep::InvGaussDensity::pi' of non-integral type [-fpermissive] 89 | static const double pi = 3.14159265358979; //!< math.constant \f$\pi\f$ @@ -2247,8 +2282,10 @@ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/LogNormDensity.hh:81:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::LogNormDensity::pi' of non-integral type [-fpermissive] 81 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. | ^~ -[ 94%] Building C object src/cxx/tools/chainsaw/CMakeFiles/chainsaw.dir/cmdline.c.o -cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/chainsaw && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/chainsaw -I/build/prime-phylo-1.0.11/src/cxx/tools/chainsaw -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -pthread -o CMakeFiles/chainsaw.dir/cmdline.c.o -c /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/chainsaw/cmdline.c +In file included from /build/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc:22: +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.hh:83:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::SiteRateHandler::MAX' of non-integral type [-fpermissive] + 83 | static const Real MAX = 1e10; //!< rates do not change for alpha > MAX. + | ^~~ In file included from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochPtMaps.hh:9, from /build/prime-phylo-1.0.11/src/cxx/libraries/prime/EpochDLTRS.hh:11, from /build/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:11: @@ -2382,20 +2419,20 @@ /build/prime-phylo-1.0.11/src/cxx/libraries/prime/LogNormDensity.hh:81:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::LogNormDensity::pi' of non-integral type [-fpermissive] 81 | static const Real pi = 3.14159265358979; //! math. constant \f$ \pi \f$. | ^~ -In file included from /build/prime-phylo-1.0.11/src/cxx/applications/primeDLRS/primeDLRS.cc:22: -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.hh:83:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::SiteRateHandler::MAX' of non-integral type [-fpermissive] - 83 | static const Real MAX = 1e10; //!< rates do not change for alpha > MAX. - | ^~~ -In file included from /build/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:23: -/build/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.hh:83:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::SiteRateHandler::MAX' of non-integral type [-fpermissive] - 83 | static const Real MAX = 1e10; //!< rates do not change for alpha > MAX. - | ^~~ +[ 95%] Building C object src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/cmdline.c.o +cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeGEM && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeGEM -I/build/prime-phylo-1.0.11/src/cxx/applications/primeGEM -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -pthread -o CMakeFiles/primeGEM.dir/cmdline.c.o -c /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeGEM/cmdline.c /build/prime-phylo-1.0.11/src/cxx/applications/primeGEM/troyo.cc: In function 'int main(int, char**)': /build/prime-phylo-1.0.11/src/cxx/applications/primeGEM/troyo.cc:197:18: warning: catching polymorphic type 'class beep::AnError' by value [-Wcatch-value=] 197 | catch(AnError e) | ^ -[ 95%] Building C object src/cxx/tools/reroot/CMakeFiles/reroot.dir/cmdline.c.o -cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reroot && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reroot -I/build/prime-phylo-1.0.11/src/cxx/tools/reroot -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -pthread -o CMakeFiles/reroot.dir/cmdline.c.o -c /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reroot/cmdline.c +In file included from /build/prime-phylo-1.0.11/src/cxx/applications/primeDTLSR/idolatrous.cc:23: +/build/prime-phylo-1.0.11/src/cxx/libraries/prime/SiteRateHandler.hh:83:23: warning: 'constexpr' needed for in-class initialization of static data member 'const Real beep::SiteRateHandler::MAX' of non-integral type [-fpermissive] + 83 | static const Real MAX = 1e10; //!< rates do not change for alpha > MAX. + | ^~~ +[ 95%] Building CXX object src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/reconcile.cc.o +cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile && /usr/bin/c++ -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile -I/build/prime-phylo-1.0.11/src/cxx/tools/reconcile -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -pthread -o CMakeFiles/reconcile.dir/reconcile.cc.o -c /build/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc +[ 96%] Building C object src/cxx/tools/reconcile/CMakeFiles/reconcile.dir/cmdline.c.o +cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile -I/build/prime-phylo-1.0.11/src/cxx/tools/reconcile -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -pthread -o CMakeFiles/reconcile.dir/cmdline.c.o -c /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile/cmdline.c /build/prime-phylo-1.0.11/src/cxx/tools/reroot/reroot.cc: In function 'int main(int, char**)': /build/prime-phylo-1.0.11/src/cxx/tools/reroot/reroot.cc:76:13: warning: enumeration value 'input_format__NULL' not handled in switch [-Wswitch] 76 | switch(args_info.input_format_arg) @@ -2403,24 +2440,11 @@ /build/prime-phylo-1.0.11/src/cxx/tools/reroot/reroot.cc:181:18: warning: catching polymorphic type 'class beep::AnError' by value [-Wcatch-value=] 181 | catch (AnError e) { | ^ -[ 96%] Building C object src/cxx/applications/primeGEM/CMakeFiles/primeGEM.dir/cmdline.c.o -cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeGEM && /usr/bin/cc -DBOOST_ALL_NO_LIB -DBOOST_MPI_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeGEM -I/build/prime-phylo-1.0.11/src/cxx/applications/primeGEM -I/usr/lib/aarch64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/build/prime-phylo-1.0.11/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime -I/build/prime-phylo-1.0.11/src/cxx/libraries -isystem /usr/lib/aarch64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/aarch64-linux-gnu/openmpi/include -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -fexceptions -g -pthread -o CMakeFiles/primeGEM.dir/cmdline.c.o -c /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeGEM/cmdline.c [ 96%] Linking CXX executable primeGEM cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeGEM && /usr/bin/cmake -E cmake_link_script CMakeFiles/primeGEM.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic -pthread CMakeFiles/primeGEM.dir/troyo.cc.o CMakeFiles/primeGEM.dir/cmdline.c.o -o primeGEM -Wl,-rpath,/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime:/usr/lib/aarch64-linux-gnu/openmpi/lib:/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/aarch64-linux-gnu/libboost_mpi.so.1.74.0 /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.74.0 ../../libraries/sfile/libprime-phylo-sfile.so make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' [ 96%] Built target primeGEM -/build/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc: In function 'int main(int, char**)': -/build/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc:37:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] - 37 | char *ofilename = "mpr.out"; - | ^~~~~~~~~ -/build/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc:128:18: warning: catching polymorphic type 'class beep::AnError' by value [-Wcatch-value=] - 128 | catch (AnError e) { - | ^ -/build/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc: In function 'void populateGsMap(beep::Tree, beep::StrStrMap&)': -/build/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc:157:23: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] - 157 | for (int i = 0; i < gtree.getNumberOfNodes(); i++) { - | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ /build/prime-phylo-1.0.11/src/cxx/tools/chainsaw/chainsaw.cc: In function 'beep::Tree ReadGuestTree(gengetopt_args_info&, std::vector*, beep::StrStrMap*)': /build/prime-phylo-1.0.11/src/cxx/tools/chainsaw/chainsaw.cc:90:9: warning: enumeration value 'guest_tree_format__NULL' not handled in switch [-Wswitch] 90 | switch(ai.guest_tree_format_arg) @@ -2436,21 +2460,32 @@ /build/prime-phylo-1.0.11/src/cxx/tools/chainsaw/chainsaw.cc:188:18: warning: catching polymorphic type 'class beep::AnError' by value [-Wcatch-value=] 188 | catch (AnError e) { | ^ -[ 97%] Linking CXX executable reroot +/build/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc: In function 'int main(int, char**)': +/build/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc:37:21: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] + 37 | char *ofilename = "mpr.out"; + | ^~~~~~~~~ +/build/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc:128:18: warning: catching polymorphic type 'class beep::AnError' by value [-Wcatch-value=] + 128 | catch (AnError e) { + | ^ +/build/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc: In function 'void populateGsMap(beep::Tree, beep::StrStrMap&)': +/build/prime-phylo-1.0.11/src/cxx/tools/reconcile/reconcile.cc:157:23: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] + 157 | for (int i = 0; i < gtree.getNumberOfNodes(); i++) { + | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 97%] Linking CXX executable chainsaw +cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/chainsaw && /usr/bin/cmake -E cmake_link_script CMakeFiles/chainsaw.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic -pthread CMakeFiles/chainsaw.dir/chainsaw.cc.o CMakeFiles/chainsaw.dir/cmdline.c.o -o chainsaw -Wl,-rpath,/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime:/usr/lib/aarch64-linux-gnu/openmpi/lib:/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/aarch64-linux-gnu/libboost_mpi.so.1.74.0 /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.74.0 ../../libraries/sfile/libprime-phylo-sfile.so +[ 98%] Linking CXX executable reroot cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reroot && /usr/bin/cmake -E cmake_link_script CMakeFiles/reroot.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic -pthread CMakeFiles/reroot.dir/reroot.cc.o CMakeFiles/reroot.dir/cmdline.c.o -o reroot -Wl,-rpath,/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime:/usr/lib/aarch64-linux-gnu/openmpi/lib:/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/aarch64-linux-gnu/libboost_mpi.so.1.74.0 /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.74.0 ../../libraries/sfile/libprime-phylo-sfile.so make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' -[ 97%] Built target reroot -[ 97%] Linking CXX executable reconcile +[ 98%] Built target chainsaw +make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' +[ 98%] Built target reroot +[ 98%] Linking CXX executable reconcile cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/reconcile && /usr/bin/cmake -E cmake_link_script CMakeFiles/reconcile.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic -pthread CMakeFiles/reconcile.dir/Rootalyzer.cc.o CMakeFiles/reconcile.dir/reconcile.cc.o CMakeFiles/reconcile.dir/cmdline.c.o -o reconcile -Wl,-rpath,/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime:/usr/lib/aarch64-linux-gnu/openmpi/lib:/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/aarch64-linux-gnu/libboost_mpi.so.1.74.0 /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.74.0 ../../libraries/sfile/libprime-phylo-sfile.so make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' -[ 97%] Built target reconcile -[ 98%] Linking CXX executable chainsaw -cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/tools/chainsaw && /usr/bin/cmake -E cmake_link_script CMakeFiles/chainsaw.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic -pthread CMakeFiles/chainsaw.dir/chainsaw.cc.o CMakeFiles/chainsaw.dir/cmdline.c.o -o chainsaw -Wl,-rpath,/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime:/usr/lib/aarch64-linux-gnu/openmpi/lib:/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile: ../../libraries/prime/libprime-phylo.so -llapack -lblas -lxml2 /usr/lib/aarch64-linux-gnu/libboost_mpi.so.1.74.0 /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.74.0 ../../libraries/sfile/libprime-phylo-sfile.so -make[3]: Leaving directory '/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu' -[ 98%] Built target chainsaw +[ 98%] Built target reconcile [ 99%] Linking CXX executable primeDLRS cd /build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/applications/primeDLRS && /usr/bin/cmake -E cmake_link_script CMakeFiles/primeDLRS.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/prime-phylo-1.0.11=. -fstack-protector-strong -Wformat -Werror=format-security -fpermissive -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -Wl,-z,relro -Wl,-z,now -rdynamic -pthread CMakeFiles/primeDLRS.dir/primeDLRS.cc.o -o primeDLRS -Wl,-rpath,/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/prime:/build/prime-phylo-1.0.11/obj-aarch64-linux-gnu/src/cxx/libraries/sfile:/usr/lib/aarch64-linux-gnu/openmpi/lib: ../../libraries/prime/libprime-phylo.so ../../libraries/sfile/libprime-phylo-sfile.so -llapack -lblas -lxml2 /usr/lib/aarch64-linux-gnu/libboost_mpi.so.1.74.0 /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/aarch64-linux-gnu/openmpi/lib/libmpi.so /usr/lib/aarch64-linux-gnu/libboost_serialization.so.1.74.0 @@ -2538,10 +2573,10 @@ dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so' -dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so' -dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so' +dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so' +dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo-sfile.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so' dpkg-shlibdeps: warning: can't extract name and version from library name 'libprime-phylo.so' @@ -2563,12 +2598,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/3522/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3522/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/1267 and its subdirectories -I: Current time: Tue Aug 24 15:36:18 -12 2021 -I: pbuilder-time-stamp: 1629862578 +I: removing directory /srv/workspace/pbuilder/3522 and its subdirectories +I: Current time: Wed Sep 28 00:03:15 +14 2022 +I: pbuilder-time-stamp: 1664272995